Contacts of the helix formed by residues 391 - 411 (chain B) in PDB entry 1T0H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 391 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389B GLU* 3.3 5.7 - - - +
390B ASN* 1.3 80.5 - - + +
392B LEU* 1.3 66.4 + - - +
393B GLU* 4.5 8.7 - - + +
394B ASP* 2.8 49.5 + - - +
395B ALA* 3.1 10.4 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B MSE 5.2 1.3 - - - +
248B ALA* 3.9 32.8 - - + +
249B LEU* 4.3 12.3 - - + -
389B GLU 5.5 0.4 - - - -
390B ASN 3.5 5.3 + - - -
391B GLN* 1.3 70.3 - - - +
393B GLU* 1.3 72.2 + - + +
395B ALA* 3.1 9.1 + - + +
396B CYS* 2.9 49.9 + - - -
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Residues in contact with GLU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B GLN* 3.2 8.6 - - + +
392B LEU* 1.3 91.8 + - + +
394B ASP* 1.3 60.1 + - - +
396B CYS* 3.4 9.0 + - - +
397B GLU* 3.0 34.6 + - + +
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Residues in contact with ASP 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLU* 3.9 20.1 - - + +
391B GLN* 2.8 43.1 + - - +
393B GLU* 1.3 76.5 - - - +
395B ALA* 1.3 63.3 + - - +
397B GLU* 3.5 6.3 + - - +
398B HIS* 3.1 24.1 + - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 4.6 9.0 - - + -
387B LEU* 3.6 24.6 - - + +
389B GLU* 3.6 30.0 - - + +
391B GLN 3.1 11.1 + - - +
392B LEU* 3.1 13.0 + - + +
394B ASP* 1.3 76.2 - - - +
396B CYS* 1.3 57.4 + - - +
398B HIS* 3.3 3.5 + - - +
399B LEU* 2.9 27.4 + - - +
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Residues in contact with CYS 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ALA 4.8 1.8 - - - -
249B LEU* 4.0 17.3 - - - -
252B PHE* 3.1 62.0 - - + -
392B LEU* 2.9 34.5 + - - -
393B GLU* 3.5 12.1 - - - +
394B ASP 3.3 0.2 - - - -
395B ALA* 1.3 77.8 - - - +
397B GLU* 1.3 56.9 - - + +
399B LEU* 3.4 4.3 + - - +
400B ALA* 2.9 23.7 + - - +
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Residues in contact with GLU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 4.5 10.4 - - - -
256B ARG* 2.6 36.3 + - - -
393B GLU* 3.0 21.6 + - + +
394B ASP* 4.0 7.0 - - - +
395B ALA 3.3 0.2 - - - -
396B CYS* 1.3 74.9 - - - +
398B HIS* 1.3 60.2 + - - +
400B ALA* 3.4 1.4 + - - +
401B ASP* 2.9 43.4 + - - +
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Residues in contact with HIS 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B VAL* 3.8 19.7 - - + +
386B ILE 3.2 24.5 + - - -
387B LEU* 3.8 4.7 - - + +
388B ASP* 5.6 0.4 - - - -
389B GLU* 2.6 28.7 + - - +
394B ASP 3.1 18.0 + - - +
395B ALA 3.3 4.7 + - - +
397B GLU* 1.3 73.2 - - - +
399B LEU* 1.3 65.0 + - - +
401B ASP* 3.4 9.4 + - + +
402B TYR* 3.2 20.4 + + + +
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Residues in contact with LEU 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 5.3 1.6 - - + -
231B LEU* 5.1 5.6 - - + -
249B LEU* 4.7 16.4 - - + -
252B PHE* 5.4 1.6 - - + -
253B LEU* 3.9 31.2 - - + -
339B VAL* 4.0 33.0 - - + -
385B VAL* 4.7 11.2 - - + -
387B LEU* 3.9 20.3 - - + +
395B ALA 2.9 17.1 + - - +
396B CYS* 3.7 5.4 - - - +
398B HIS* 1.3 76.4 - - - +
400B ALA* 1.3 58.4 + - - +
402B TYR* 3.2 6.5 + - - +
403B LEU* 3.0 49.4 + - + +
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Residues in contact with ALA 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B PHE* 3.9 12.0 - - + -
256B ARG* 3.7 40.2 - - + +
257B PHE* 3.7 13.3 - - + -
396B CYS 2.9 18.1 + - - +
397B GLU 3.7 4.3 - - - +
399B LEU* 1.3 77.6 - - - +
401B ASP* 1.3 57.0 + - - +
403B LEU 3.3 0.5 + - - -
404B GLU* 2.8 36.0 + - - +
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Residues in contact with ASP 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 4.8 3.1 + - - -
397B GLU* 2.9 33.8 + - - +
398B HIS* 3.6 8.5 - - + +
399B LEU 3.4 0.2 - - - -
400B ALA* 1.3 76.6 - - - +
402B TYR* 1.3 62.8 + - - +
404B GLU* 3.4 7.8 + - - +
405B ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B ARG* 4.6 5.9 + - - -
337B ILE* 3.8 28.0 - - + +
384B ASP* 3.6 35.6 + - + +
385B VAL* 3.5 35.4 - - + -
398B HIS* 3.2 14.1 + - + +
399B LEU* 3.2 8.5 + - + +
401B ASP* 1.3 77.4 - - - +
403B LEU* 1.3 70.2 + - + +
405B ALA* 3.3 7.7 + - + +
406B TYR* 3.1 30.2 + + + +
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B VAL* 3.8 30.7 - - + -
253B LEU* 3.9 33.2 - - + -
257B PHE* 3.8 20.8 - - + -
261B ILE* 5.7 1.8 - - + -
315B LEU* 4.3 23.9 - - + +
317B VAL* 5.6 2.2 - - + -
337B ILE* 4.6 7.6 - - + -
399B LEU* 3.0 34.5 + - + +
402B TYR* 1.3 91.1 - - + +
404B GLU* 1.3 61.0 + - - +
406B TYR* 3.7 4.9 - - + +
407B TRP* 2.9 28.2 + - - +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 3.1 27.4 + - - +
257B PHE* 3.4 12.7 - - + -
260B ARG* 3.0 37.7 + - - -
400B ALA 2.8 26.1 + - - +
401B ASP* 3.8 7.9 - - - +
403B LEU* 1.3 75.9 - - - +
405B ALA* 1.3 61.1 + - - +
407B TRP* 3.3 6.9 + - - +
408B LYS* 3.1 44.0 + - - +
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Residues in contact with ALA 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLU* 3.2 24.7 - - - +
401B ASP 3.1 13.9 + - - +
402B TYR* 3.7 10.3 - - + +
404B GLU* 1.3 77.2 - - - +
406B TYR* 1.3 56.3 - - - +
408B LYS* 3.3 6.3 + - - +
409B ALA* 3.0 24.3 + - - +
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A HIS* 5.6 0.7 - - - -
109A VAL* 4.4 11.1 - - + +
225B SER 4.2 2.1 + - - -
226B MSE 3.6 25.9 - - + -
227B ARG* 2.9 56.5 + - + +
315B LEU* 4.0 18.6 - - + -
337B ILE* 3.8 22.9 - - + -
402B TYR* 3.1 25.8 + + + +
403B LEU* 3.7 7.9 - - + +
404B GLU 3.3 0.2 - - - -
405B ALA* 1.3 74.6 - - - +
407B TRP* 1.3 61.3 + - - +
409B ALA* 3.2 9.6 + - + +
410B THR* 2.8 45.6 + - + +
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Residues in contact with TRP 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B MSE 4.4 2.5 - - + -
260B ARG* 3.7 67.2 - - + +
313B LEU 3.6 11.0 - - - -
314B GLN* 4.0 10.8 - - - -
315B LEU* 3.7 25.6 - - + -
403B LEU 2.9 15.3 + - - +
404B GLU* 3.5 14.1 - - - +
406B TYR* 1.3 75.8 - - - +
408B LYS* 1.3 64.7 + - + +
410B THR* 3.1 7.6 + - - -
411B HIS* 2.7 76.6 + + + +
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 5.0 1.2 + - - -
111A GLU* 3.7 32.0 - - + +
404B GLU* 3.1 36.9 + - - +
405B ALA* 3.6 9.6 - - - +
407B TRP* 1.3 80.1 - - + +
409B ALA* 1.3 65.6 + - - +
410B THR 3.3 0.3 + - - -
411B HIS 3.4 21.1 + - - +
412B PRO* 4.1 3.5 - - - +
413B PRO* 5.6 1.2 - - - +
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Residues in contact with ALA 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG* 2.8 35.3 + - - -
109A VAL* 3.8 16.8 - - + +
110A LYS* 3.7 9.2 + - - -
111A GLU* 3.8 24.8 - - + +
405B ALA 3.0 13.6 + - - +
406B TYR* 3.2 16.1 + - + +
408B LYS* 1.3 78.9 - - - +
410B THR* 1.3 51.2 + - - +
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Residues in contact with THR 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A HIS* 4.3 14.7 - - - +
107A ARG* 3.9 7.0 + - - +
109A VAL* 3.7 17.9 - - + -
226B MSE 3.6 33.6 - - - +
313B LEU* 4.1 9.0 - - - +
406B TYR* 2.8 49.2 + - + +
407B TRP* 3.1 10.4 + - - -
408B LYS 3.2 0.2 - - - -
409B ALA* 1.3 76.5 - - - +
411B HIS* 1.3 73.5 + - - +
412B PRO* 3.7 8.1 - - - +
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Residues in contact with HIS 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 2.9 53.8 + - + +
407B TRP* 2.7 67.6 + + + +
408B LYS* 3.4 14.8 + - - +
410B THR* 1.3 104.7 + - - +
412B PRO* 1.3 70.8 - - + +
413B PRO* 3.4 4.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il